So the software is pretty much just the working tool for the publisher. Anything imported or exported should be converted to a pdf.

Do I have that right?

I think you had the basic idea from the beginning. You create your document with your software (InDesign, Quark, etc.). When you are done, you "export" to EPS or PDF and send this to the print house. And if you need to make changes, you change the original and translate again.

That's the simple version. But check with your print house about what they like.